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CausalR (version 1.4.3)

Causal Reasoning Methods

Description

Causal reasoning methods for biological networks, to enable regulator prediction and reconstruction of regulatory networks from high dimensional data.

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Version

Version

1.4.3

License

GPL (>= 2)

Maintainer

Glyn Bradley

Last Published

February 15th, 2017

Functions in CausalR (1.4.3)

CalculateEnrichmentPValue

calculates an enrichment p-value
AddIDsToVertices

add IDs to vertices
AddWeightsToEdges

add weights to edges
CalculateWeightGivenValuesInThreeByThreeContingencyTable

calculate weight given values in three-by-three contingency table
CausalR-package

The CausalR package
GetNodeID

get CCG node ID
GetNodeName

get node name
GetApproximateMaximumDValueFromTwoByTwoContingencyTable

computes an approximate maximum D value or weight
GetCombinationsOfCorrectandIncorrectPredictions

returns table of correct and incorrect predictions
GetWeightsAboveHypothesisScoreForAThreeByTwoTable

updates weights for contingency table and produce values for p-value calculation
GetWeightsAboveHypothesisScoreAndTotalWeights

get weights above hypothesis score and total weights
GetWeightsFromInteractionInformation

get weights from interaction information
MakePredictions

make predictions
runRankHypothesis

run rank the hypothesis
RemoveIDsNotInExperimentalData

remove IDs not in experimental data
CalculateSignificanceUsingCubicAlgorithm

calculate significance using the cubic algorithm
CalculateSignificanceUsingCubicAlgorithm1b

Calculate Significance Using Cubic Algorithm
CheckPossibleValuesAreValid

check possible values are valid
GetApproximateMaximumDValueFromThreeByTwoContingencyTable

returns approximate maximum D value or weight for a 3x2 superfamily
GetAllPossibleRoundingCombinations

get score for numbers of correct and incorrect predictions
CheckRowAndColumnSumValuesAreValid

check row and column sum values are valid
CompareHypothesis

compare hypothesis
GetPathsInSifFormat

Get paths in Sif format
GetNumberOfPositiveAndNegativeEntries

counts the number of positive and negative entries
ComputeFinalDistribution

compute final distribution
GetShortestPathsFromCCG

get shortest paths from CCG
GetWeightForNumbersOfCorrectandIncorrectPredictions

get weight for numbers of correct and incorrect predictions
ProcessExperimentalData

process experimental data
WriteExplainedNodesToSifFile

Write explained nodes to Sif file
RankTheHypotheses

rank the hypotheses
CreateCG

create a Computational Graph (CG)
CalculateSignificance

calculate overall significance p-value
FindIdsOfConnectedNodesInSubgraph

find Ids of connected nodes in subgraph
CreateNetworkFromTable

create network from table
FindMaximumDValue

find maximum D value
GetMatrixOfCausalRelationships

compute causal relationships matrix
GetMaxDValueForAFamily

get maximun D value for a family
GetScoresWeightsMatrixByCubicAlg

get scores weights matrix by the cubic algorithm
PopulateTheThreeByThreeContingencyTable

populate the three-by-three contingency table
GetScoresWeightsMatrix

get scores weight matrix
PopulateTwoByTwoContingencyTable

Populate Two by Two Contingency Table
ReadSifFileToTable

read .sif to Table
ReadExperimentalData

read experimental data
AnalyseExperimentalData

analyse experimental data
AnalysePredictionsList

analyse predictions list
ComputePValueFromDistributionTable

compute a p-value from the distribution table
GetExplainedNodesOfCCG

Get explained nodes of CCG
CreateCCG

create a Computational Causal Graph (CCG)
GetInteractionInformation

returns interaction information from input data
GetRegulatedNodes

get regulated nodes
GetRowAndColumnSumValues

get row and column sum values
GetScoresForSingleNode

Get scores for single node
GetScoreForNumbersOfCorrectandIncorrectPredictions

returns the score for a given number of correct and incorrect predictions
MakePredictionsFromCCG

make predictions from CCG
MakePredictionsFromCG

make predictions from CG
runSCANR

run ScanR
ScoreHypothesis

score hypothesis
CalculateSignificanceUsingQuarticAlgorithm

calculate significance using the quartic algorithm
CalculateTotalWeightForAllContingencyTables

calculate total weight for all contingency tables
DetermineInteractionTypeOfPath

determine interaction type of path
FindApproximateValuesThatWillMaximiseDValue

find approximate values that will maximise D value
GetMaxDValueForAThreeByTwoFamily

get maximum D value for three-by-two a family
GetSetOfDifferentiallyExpressedGenes

get set of differientially expressed genes
GetMaximumDValueFromTwoByTwoContingencyTable

get maximum D value from two-by-two contingency table
GetSetOfSignificantPredictions

get set of significant predictions
OrderHypotheses

order hypotheses
PlotGraphWithNodeNames

plot graph with node names
ValidateFormatOfDataTable

validate format of the experimental data table
ValidateFormatOfTable

validate format of table